The only difference is a slightly higher temp rating between 3 and 4. There is no chemical reaction possible from DOT 3 that will affect that DOT 4 master cylinder internals, so choose either sticking with DOT 3, or change to DOT 4.
Your system will need a full bleed anyway so put the fresh stuff through the entire system (your choice of 3 or 4) and don't worry about any residual DOT 3 in the lines if you switch to DOT 4.